Package: bamsignals 1.39.0

Johannes Helmuth

bamsignals: Extract read count signals from bam files

This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.

Authors:Alessandro Mammana [aut, cre], Johannes Helmuth [aut]

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bamsignals.pdf |bamsignals.html✨
bamsignals/json (API)
NEWS

# Install 'bamsignals' in R:
install.packages('bamsignals', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lamortenera/bamsignals/issues

Uses libs:
  • curl– Easy-to-use client-side URL transfer library
  • bzip2– High-quality block-sorting file compressor library
  • xz-utils– XZ-format compression library
  • zlib– Compression library
  • c++– GNU Standard C++ Library v3

On BioConductor:bamsignals-1.39.0(bioc 3.21)bamsignals-1.38.0(bioc 3.20)

dataimportsequencingcoveragealignmentcurlbzip2xz-utilszlibcpp

8.95 score 14 stars 11 packages 31 scripts 1.5k downloads 5 mentions 6 exports 20 dependencies

Last updated 3 months agofrom:df2b237eef. Checks:3 OK, 6 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 06 2025
R-4.5-win-x86_64OKJan 06 2025
R-4.5-linux-x86_64OKJan 06 2025
R-4.4-win-x86_64NOTEJan 06 2025
R-4.4-mac-x86_64NOTEJan 06 2025
R-4.4-mac-aarch64NOTEJan 06 2025
R-4.3-win-x86_64NOTEJan 06 2025
R-4.3-mac-x86_64NOTEJan 06 2025
R-4.3-mac-aarch64NOTEJan 06 2025

Exports:alignSignalsas.listbamCountbamCoveragebamProfilewidth

Dependencies:askpassBiocGenericscurlgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitemimeopensslR6RcppRhtslibS4VectorssysUCSC.utilsXVectorzlibbioc

Introduction to the bamsignals package

Alessandro Mammana and Johannes Helmuth

Rendered frombamsignals.Rmdusingknitr::rmarkdownon Jan 06 2025.

Last update: 2016-04-11
Started: 2015-02-13

Readme and manuals

Help Manual

Help pageTopics
Converts the container to a list 'l' such that 'l[[i]]' is the i-th signal.as.list.CountSignals
Efficient counting of reads in a bam filebamsignals-package bamsignals
Functions for extracting count signals from a bam file.bamCount bamCount,character,GenomicRanges-method bamCoverage bamCoverage,character,GenomicRanges-method bamProfile bamProfile,character,GenomicRanges-method bamsignals-methods
Container for count signalsalignSignals alignSignals,CountSignals-method as.list as.list,CountSignals-method CountSignals CountSignals-class length length,CountSignals-method width width,CountSignals-method [,CountSignals,ANY-method